Cytomegalovirus (CMV) is a significant cause of mortality and morbidity in immunocompromised patients and an important cause of birth defects if acquired in utero. The licensed CMV antivirals, ganciclovir, cidofovir and foscarnet, all target the viral DNA polymerase. For each drug prolonged use is associated with significant toxicities and development of drug resistance. None are approved for use during pregnancy. Therefore, development of new anti-CMV drugs that target different pathways would be beneficial. All herpesviruses encode an alkaline nuclease. That genetic disruption of the CMV alkaline nuclease, UL98, reduces CMV replication by 1,000-fold suggests that UL98 may be a useful target for development of novel anti-CMV drugs. Moreover, using herpes simplex virus type 1 Hsiang and Ho found that the anthraquinone emodin inhibits activity of the viral alkaline nuclease, blocks viral replication in cell culture, and reduces viral pathogeneses in a mouse model (Brit. J. of Pharm., 2008). Earlier studies also showed that anthraquinone derivatives including emodin have anti-CMV activity (Barnard et al., Antiviral Research 1992 & 1995), although the mechanism of CMV inhibition has not been further studied. We therefore sought to confirm the anti-CMV activities of emodin and related anthraquinone derivatives, to characterize their mechanisms of action, and to determine specifically if they act through inhibition of UL98. Using a luciferase-based CMV yield reduction assay emodin inhibited CMV replication (IC50 = 4.9 μM); however, that the TD50 for cytotoxicity (determined using an luciferase-based cell viability assay) was only 2-fold higher suggested that emodin may act non-specifically. Two additional anthraquinone derivatives (acid blue 40 and alizarin violet R) inhibited CMV only at high concentrations (IC50 = 238; 265 μM) that were also cytotoxic. Atanyl blue PRL, however, exhibited anti-CMV activity (IC50 = 6.3 μM) with low cytotoxicity (TD50 = 216 μM). Thus, characterization of atanyl blue PRL (impact on gene expression, GFP expression, viral spread, infectivity, time of addition studies, and inhibition of UL98 nuclease activity) should be informative. Atanyl blue PRL appears to block immediate-early gene expression and reduce early and late gene expression. Atanyl blue PRL also blocked GFP expression, reduced viral spread, and also lowered the infectivity of CMV. Finally, atanyl blue PRL inhibits UL98 alkaline nuclease activity at an IC50 of 5.7 μM. This suggests that atanyl blue PRL may inhibit CMV through inhibition of UL98. Thus, atanyl blue PRL represents a novel class of anti-herpesvirals and provides a lead structure for structure based drug discovery.

Computationally driven drug design/discovery efforts generally rely on accurate assessment of the forces that guide the molecular recognition process. HINT (Hydropathic INTeraction) is a natural force field, derived from experimentally determined partition coefficients that quantifies all non-bonded interactions in the biological environment, including hydrogen bonding, electrostatic and hydrophobic interactions, and the energy of desolvation. The overall goal of this work is to apply the HINT-based atomic level description of molecular systems to biologically important proteins, to better understand their biochemistry – a key step in exploiting them for therapeutic purposes. This dissertation discusses the results of three diverse projects: i) structural modeling of human sphingosine kinase 2 (SphK2, a novel anticancer target) and binding mode determination of an isoform selective thiazolidine-2,4-dione (TZD) analog; ii) structural modeling of human cytomegalorvirus (HCMV) alkaline nuclease (AN) UL98 (a novel antiviral target) and subsequent virtual screening of its active site; and iii) explicit treatment of interfacial waters during protein-protein docking process using HINT-based computational tools. SphK2 is a key regulator of the sphingosine-rheostat, and its upregulation /overexpression has been associated with cancer development. We report structural modeling studies of a novel TZD-analog that selectively inhibits SphK2, in a HINT analysis that identifies the key structural features of ligand and protein binding site responsible for isoform selectivity. The second aim was to build a three-dimensional structure of a novel HCMV target – AN UL98, to identify its catalytically important residues. HINT analysis of the interaction of 5’ DNA end at its active site is reported. A parallel aim to perform in silico screening with a site-based pharmacophore model, identified several novel hits with potentially desirable chemical features for interaction with UL98 AN. The majority of current protein-protein docking algorithms fail to account for water molecules involved in bridging interactions between partners, mediating and stabilizing their association. HINT is capable of reproducing the physical and chemical properties of such waters, while accounting for their energetic stabilizing contributions. We have designed a solvated protein-protein docking protocol that explicitly models the Relevant bridging waters, and demonstrate that more accurate results are obtained when water is not ignored.